Inhibition of enteropathogenic Escherichia coli biofilm formation by DNA aptamer

Molecular Biology Reports - Enteropathogenic Escherichia coli (EPEC) is a bioagent that causes diarrhea through the formation of biofilm. The recalcitrant of EPEC to the current conventional...     

Label-free capacitive DNA sensor using immobilized pyrrolidinyl PNA probe: Effect of the length and terminating head group of the blocking thiols

This paper reports, for the first time, the influence of the length and the terminating head group of blocking thiols on the sensitivity and specificity of a label-free capacitive DNA detection system using immobilized pyrrolidinyl peptide nucleic acid (acpcPNA) probes. A C-terminal lysine-modified acpcPNA was immobilized through four different alkanethiol self-assembled monolayers (SAMs), i.e., 3-mercaptopropionic acid (MPA), thioctic acid (TA), thiourea (TU) and mercaptosuccinic acid (MSA). The hybridization between the acpcPNA probes and the target DNA was directly measured using the capacitive system. Five blocking thiols of various lengths (C=3, 6, 8, 9 and 11), with the -OH terminating head group, i.e., 3-mercapto-1-propanol (3-MPL), 6-mercapto-1-hexanol (6-MHL), 8-mercapto-1-octanol (8-MOL), 9-mercapto-1-nonanol (9-MNL), 11-mercapto-1-undecanol (11-MUL) and another blocking thiol (C=11) with a -CH(3) terminating head group, and 1-dodecanethiol (1-DDT) were investigated. The blocking thiol with the same length as the total spacer of the immobilized acpcPNA gave the highest sensitivity and specificity with the -OH terminating head group providing a slightly better signal than the -CH(3) group. Under the optimized conditions, the immobilized acpcPNA probes provided a wide linear range for DNA detection (1.0×10(-11)-1.0×10(-8)M) with a very low detection limit in the picomolar range. The modified acpcPNA electrode could be reused through at least 58 cycles. The high sensitivity and very low detection limits are potentially useful for the analysis of ultra-trace levels of DNA in samples. Preliminary studies were also performed to see the effect of probe concentration and target length.     

Ultra trace analysis of small molecule by label-free impedimetric immunosensor using multilayer modified electrode

A multilayer electrode modified with a self-assembled thiourea monolayer (SATUM) followed by gold nanoparticles (AuNPs), mercaptosuccinic acid (MSA) and antibody was investigated for the detection of ultra trace amount of a small molecule (chloramphenicol) in an impedimetric system. The formation of the antibody-antigen complex at the electrode surface caused the impedance to increase. Under optimum conditions three modified electrodes were compared the SATUM/AuNPs/MSA electrode provided a wide linear range (0.50-10) × 10?1? M, and a very low determination limit of 1.0 × 10?1? M. This determination limit was much lower than the SATUM/AuNPs electrode, 1.0 × 10?1? M, and SATUM electrode, 4.7 × 10?1? M. The modified electrode provided good selectivity for chloramphenicol detection and can be reused up to 45 times with a relative standard deviation of lower than 4%. When applied to determine chloramphenicol in shrimp samples, the results agreed well with those obtained by the high-performance liquid chromatography coupled with a photo diode array detector (P > 0.05). The developed system can be applied to detect other small molecules using appropriate affinity binding pairs.     

Gold nanoparticles (AuNP)-based aptasensor for enteropathogenic Escherichia coli detection

Molecular Biology Reports - Diarrhea is a major cause of severe gastrointestinal illness in the infant especially in many developing countries. Although this molecular technique has been accepted...     

Collagen type IX: Evidence for covalent linkages to type II collagen in cartilage

A major site of pyridinoline cross-linking in bovine type IX collagen was traced to a tryptic peptide derived from one of the molecule's HMW chains. This peptide gave two amino acid sequences (in 2/1 ratio) consistent with it being a three-chained structure. The major sequence matched exactly that of the C-telopeptide of type II collagen from the same tissue. A second HMW chain that contained pyridinoline cross-links also gave two amino-terminal sequences, one from its own amino terminus, the other matching exactly the N-telopeptide cross-linking sequence of type II collagen. We conclude that type IX collagen molecules are covalently cross-linked in cartilage to molecules of type II collagen, probably at fibril surfaces.     

Selective metabolite and peptide capture/mass detection using fluorous affinity tags

A new and general methodology is described for the targeted enrichment and subsequent direct mass spectrometric characterization of sample subsets bearing various chemical functionalities from highly complex mixtures of biological origin. Specifically, sample components containing a chemical moiety of interest are first selectively labeled with perfluoroalkyl groups, and the entire sample is then applied to a perfluoroalkyl-silylated porous silicon (pSi) surface. Due to the unique hydrophobic and lipophobic nature of the perfluorinated tags, unlabeled sample components are readily removed using simple surface washes, and the enriched sample fraction can then directly be analyzed by desorption/ionization on silicon mass spectrometry (DIOS-MS). Importantly, this fluorous-based enrichment methodology provides a single platform that is equally applicable to both peptide as well as small molecule focused applications. The utility of this technique is demonstrated by the enrichment and mass spectrometric analysis of both various peptide subsets from protein digests as well as amino acids from serum.     

The response of salt marsh vegetation to tidal reduction caused by the Oosterschelde storm-surge barrier

In 1986 a sluice gate barrier was completed in the mouth of the Oosterschelde estuary. The barrier has been partially or completely closed during 1986 and the first months of 1987. Consequently the high tides were reduced to such a level that the salt marshes were scarcely flooded. Since April 1987 the barrier has been closed on average during two out of 706 high tides a year. Although the barrier allows tidal exchange the tidal flow has been restricted as a result of the reduced width of the mouth of the estuary. This restriction of the tidal flow caused a 26 cm decrease of mean high water in the eastern part of the estuary. As a result the inundation frequencies of the salt marshes decreased.The response of salt-marsh vegetation to this tidal reduction was analyzed using annual records (1982 till 1990) of species composition in 57 permanent plots in two marshes at the southern shore of the estuary. Analysis of the response of individual species to marsh elevation in the pre and the post-barrier situation revealed that most species moved down the marsh elevation gradient. The first axis of an ordination (DCA-1) was significantly negatively related to inundation frequency. Between 1984 and 1990 all plots were displaced towards a significantly higher ordination score, indicating a trend towards a species composition from higher up the marsh. The position of most plots along DCA-1 remained stable until 1985 and started to increase in 1986 or 1987. The vegetation in plots dominated either by Halimione portulacoides or by Spartina anglica, started to change in 1985. This premature change was attributed to frost damage in January 1985. The initially high rate of change along DCA-1 decreased in 1989 and 1990. This would suggest that the vegetation re-equilibrated with the newly established tidal conditions. Further analysis revealed no significant difference in the relation between inundation frequency and sample score along DCA-1 between 1984 and 1990. This corroborates the view that species composition had re-equilibrated with the tidal conditions. Along DCA-2 the samples were displaced towards a significantly higher score as well. The change was attributed to an increase of the perennial Halimione and the annual Suaeda maritima. The annual Atriplex hastata displayed an increase from 1986 till 1988, but strongly declined in 1990. The transient response of this annual was described by DCA-3.During the pre-barrier phase several attempts had been made to predict the vegetation response to tidal reduction. We developed a multivariate model (CCA) with inundation frequency as a constraining factor to describe the relation between inundation frequency and species composition in the pre-barrier phase in 1984. Next we used this model to predict the score of the samples along CCA-1 in the post-barrier phase from the inundation frequencies in 1990. The actual ordination score in 1990 was calculated from the observed species composition. The predicted ordination scores did not differ significantly from the observed ones. In retrospect it is concluded that the response of the vegetation to the reduction of the tides, as far as the fraction of species composition which is related to inundation frequency is concerned, could have been predicted by our model.

---